Analysis of macromolecular enzymatic processes is based largely on indirect observations. We developed a direct imaging approach in which one or more macromolecular components are labeled with Quantum Dots (Q-dots), allowing one to follow the behavior of a population of individual molecules in real-time. Q-dots nano-biochemistry provides an unprecedented simple and direct analysis of macromolecular complexes in action. This system can be adapted for proteomics and drug discovery. We have chosen to pioneer the monitoring of single macromolecular events by the attachment of Q-dots to DNA, RNA and proteins without interfering with their biological activity. This method provides a missing link between analysis of complex interactions in transcription complexes in vivo (ChIP analysis) and results obtained by traditional bulk biochemistry. This system can also be adapted for proteomics and drug discovery.